Man pages for AllenInstitute/scrattch.hicat
Hierarchical Iterative Clustering Analysis for Transcriptomic data

adjust_colorCorrect duplicated colors
angleTitle
avgangleTitle
batch_processBatch process
build_dendBuild dend
build_dend_harmonizeBuild dend harmonize
build_dend_with_meansTitle
build_tsneTitle
calc_tauCalculate Tau scores for each gene
CanonCorCanon cor
CCACCA
check_donorFind donor clusters
check_neunCheck whether clusters are Neun+ or Neun-
check_outlierCheck for outlier clusters
check_qcCheck qc of numeric metric
clean_outliersTitle
collect_co_matrixCollect co-clustering matrix from results files
comb_de_resultTitle
combine_clcombine cl
compare_annotateCompare two sets of cluster assignments for the same set of...
compare_plotCompare and plot two sets of cluster assignments
compute_knncompute knn
compute_vg_statsCompute gene expression variance statistics
convert_pair_matrixConvert paired cluster comparison values to a matrix
convert_pair_matrix_strConvert paired cluster comparison values to a matrix
cpmConvert a matrix of raw counts to a matrix of Counts per...
create_pairsTitle
cutree_dendCut tree dendrogram
de_all_pairsPerform all pairwise differential expression comparison...
DE_genes_cat_by_clTitle
DE_genes_pairsreverse-compatibility wrapper around de_selected_pairs()
de_genes_pairs_multipleTitle
DE_genes_pwreverse-compatibility wrapper around de_all_pairs()
dend_lcaDend lca
dend_listDendrogram list
dend_matchDendrogram match
de_pairreverse-compatibility wrapper around score_pair_stats()
de_pair_chisqPerform pairwise differential detection tests using...
de_pair_limmaPerform pairwise DE tests using limma for a single pair of...
de_paramSet differential expression (DE) parameters for genes and...
de_scorereverse-compatibility wrapper around de_all_pairs_stats()
de_score_pairsreverse-compatibility wrapper around...
de_selected_pairsPerform pairwise differential gene expression tests between...
de_stats_all_pairsCompute differential expression summary statistics for all...
de_stats_pairCompute differential expression summary statistics based on a...
de_stats_selected_pairsCompute differential expression summary statistics for...
display_clDisplay cluster plot
display_cl4Title
display_cl_markers_co.ratioTitle
display_cl_one_vs_othersTitle
doubletFinderDoublet detection in single-cell RNA sequencing data
edgeMakerfunction to draw (curved) line between two points
fast_tsneTitle
find_doubletFind doublet
find_low_quality_clUse DEGenes to identify clusters with few differentially...
find_vgIdentify high variability genes using Brennecke's method
findVGreverse-compatibility wrapper around find_vg()
gene_dispersionCompute dispersion for each gene in a gene x sample matrix
gene_gene_cor_conservationTitle
gene_loess_fitCompute dispersion-mean Loess-fit for each gene in a gene x...
gene_loess_fit_zCompute dispersion z scores for the residuals of a loess fit
gene_meansCompute means for each gene in a gene x sample matrix
gene_varsCompute variance for each gene in a gene x sample matrix
gene_zCompute dispersion z-scores for each gene in a gene x sample...
get_beta_scoreTitle
get_cell.cl.co.ratioGet cell co-clustering ratios
get_cl_dfGenerate an initial cl.df object based on cl
get_cl_matGenerate a sparse matrix one-hot representation of clusters x...
get_cl_meansCompute cluster means for each row in a matrix
get_cl_means_listTitle
get_cl_mediansCompute cluster medians for each row in a matrix
get_cl_present_listTitle
get_cl_propCompute cluster proportions for each row in a matrix
get_cl_simTitle
get_cl_sim_multipleTitle
get_cl_sumsCompute cluster sums for each row in a matrix
get_core_intermediateGet core intermediate
get_de_genes_symGet de genes sym
get_de_lfc_listTitle
get_de_matrixGenerate a matrix of pairwise DE results
get_dend_markersget dendrogram precomputed markers
get_dend_markers_directionget dendrogram precomputed markers (direction)
get_dend_parentGet dendrogram parent
get_de_pairGet de pair
get_de_resultTitle
get_de_scoreGet de score
get_eigenCompute module eigen genes
get_gene_cl_correlationGet gene cl correlation
get_gene_scoreTitle
get_knnGet KNN
get_knn_batchget knn batch
get_knn_graphget knn graph
get_knn_weightTitle
get.markers.numTitle
get_pair_matrixSubset a matrix as a vector using row and column positions
get_pair_matrix_coorConvert matrix row/column positions to vector position
get_pairsConvert underscore_separated pair names to a data.frame
get_RD_cl_centerTitle
getTopMarkersByPropNewFind specific marker gene for each cluster
group_clAssign clusters to a group
group_specific_markersTitle
harmonizeHarmonize
heatmap.3A modified version of heatmap.2 from the gplots package for...
heatmap.4Title
i_harmonizei harmonize
impute_knnTitle
impute_knn_globalTitle
impute_val_corImpute val cor
incrementHexAdjust color vector
iter_clustIterative clustering algorithm for single cell RNAseq dataset
iter_consensus_clustIterative consensus clustering
iter_impute_knnTitle
jaccardCompute jaccard distances between columns of a matrix
jaccard_leidenPerform Jaccard/Leiden clustering
jaccard_leiden.RANNPerform Jaccard/Louvain clustering based on RANN
jaccard_louvainPerform Jaccard/Louvain clustering using Rphenograph
jaccard_louvain.RANNPerform Jaccard/Louvain clustering based on RANN
knn_corKNN cor
knn_cosineKNN cosine
knn_jaccard_louvainKNN Jaccard Louvain
knn_jointknn joint
label_dendLabel dendrogram
lm_matrixTitle
lm_normalizeadd batch substracted median
logCPMConvert a matrix of raw counts to a matrix of log2(Counts per...
makeColorsUniqueMake a vector of unique colors
makeLayerLabelNumeric layer for annotation object
makeRegionLabelSplit region from roi for annotation object
map_by_corMap samples to a training dataset by correlation
map_cl_summaryMap a dataset to a reference, and compare existing cluster...
map_cvRun a single round of cross-validation of cluster mapping...
map_dendTitle
map_dend_markersMap dend markers
map_dend_membershipTitle
mappingTitle
map_samplingPerform bootstrapped mapping using a fraction of provided...
markers_max_tauTitle
markers_tau_one_vs_otherTitle
match_clCompute correlations of clusters to a reference set, and get...
merge_clMerge clusters based on pairwise differential expressed...
merge_cl_multipleTitle
merge_knn_resultmerge knn result
multiplotTitle
mybgplot3dTitle
node_specific_markersNode specific markers
node_vs_sibling_markersNode vs sibling markers
onestep_clustOne round of clustering in the iteractive clustering pipeline
pair_corCompute correlations between each matching row or column of...
perpTitle
perpEndTitle
perpMidTitle
perpStartTitle
plot_2d_selectTitle
plot_3d_labelTitle
plot_3d_label_multipleTitle
plot_3d_selectTitle
plot_3d_valTitle
plot_cl_cellsTitle
plot_cl_heatmapTitle
plot_cl_heatmap4Title
plot_cl_lowPlot cl low
plot_cl_meta_barplotTitle
plot_confusionTitle
plot_de_lfc_numTitle
plot_dendPlot dendrogram
plot_de_numTitle
plot_doubletPlot doublet
plot_low_qcPlot low-quality clusters
plot_markersTitle
plot_markers_cl_meansPlot markers cl means
plot_pair_matrixTitle
plot_RD_clTitle
plot_RD_geneTitle
plot_RD_metaTitle
plot_tsnePlot tsne
plot_tsne_clTitle
plot_tSNE_geneTitle
plot_tSNE_metaTitle
plot_vgGenerate gene variance plots
prcomp.irlbaprcomp irlba
predict_annotate_corPredict annotations by cluster correlation
predict_knnTitle
predict_knn_newTitle
prune_dendPrune dendrogram
pvclust_show_signif_gradientPv clust show significant gradient
rd_PCATitle
refine_clRefine clusters
renameAndOrderClustersRename clusters using genes and metadata
reorder_clReorder cluster based on hiearchical clustering of clusters...
reorder_dendReorder dendrogram
reorder_factorReorder factors of one annotation to match another
rescale_samplesRescale a gene x sample matrix
resolve_clTitle
run_consensus_clustWrapper function to repeatively run clustering on subsampled...
RunUMAPAdapt from Seurat package
sample_cellsDownsample cells from each cluster
sample_sets_listSample sets lists
select_dend_markersSelect dend markers
select_joint_genesSelect joint genes
select_joint_markersTitle
select_markersTitle
select_markers_pairTitle
select_markers_pair_directionTitle
select_markers_pair_groupTitle
select_N_markersTitle
select_node_specific_markersSelect node specific markers
select_pos_dend_markersSelect pos dend markers
select_pos_markersTitle
set_pair_matrixUpdate a matrix with values from a 1d vector using row and...
sim_knnSim knn
simple_dendSimple dendrogram
sparse_corCompute correlation scores for columns of a sparse matrix
summarize_clTitle
test_knnTest knn
test_mergeTitle
unbranch_by_confUnbranch by conf
unbranch_by_lengthUnbranch by length
updateSampDatUpdate cluster names in annotation data frame
vec_chisq_testVectorized Chi-squared tests for differential gene detection
within_group_specific_markersTitle
AllenInstitute/scrattch.hicat documentation built on April 26, 2020, 4:59 a.m.